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Nano Origami for DNA, Complete With Software

ScuttleMonkey posted about 5 years ago | from the next-gen-legos dept.

Robotics 32

wisebabo writes "Some researchers at Technische Universitaet Muenchen and Harvard have developed a way to make DNA 'Origami' fold up into all sorts of desired nanoscale shapes. While this has been done before, there now seems to be a much greater assortment of shapes they can create. What's particularly interesting is that they've developed some software that can be used (presumably with a DNA assembler) that will create what you want; think of CAD/CAM on a molecular scale! 'The toolbox they have developed includes a graphical software program that helps to translate specific design concepts into the DNA programming required to realize them. Three-dimensional shapes are produced by "tuning" the number, arrangement, and lengths of helices.'"

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Well that explains it (0, Redundant)

rehtonAesoohC (954490) | about 5 years ago | (#28991075)

Superman must have been made of 1,000,000 DNA Origami cranes.

Who knew?!

Re:Well that explains it (0)

Anonymous Coward | about 5 years ago | (#29012169)

WOW.

First comment modded redundant. If that's not mod abuse, I don't know what the hell is.

Well...? (3, Insightful)

Ketto (1349749) | about 5 years ago | (#28991101)

I wonder if this is similar in scope to the microscopic engine they built a few years back... Really neat in concept and design, but of small practical significance...

Re:Well...? (1)

StellarFury (1058280) | about 5 years ago | (#28991157)

small practical significance...

Got it in one.

Johnny, what can you make of this? (1)

spun (1352) | about 5 years ago | (#28991275)

This? Why, I can make a hat, or a brooch, or a pterodactyl...

Re:Well...? (1)

shnull (1359843) | about 5 years ago | (#29008877)

does this mean we can breed women with three breasts and no mouth ?

Re:Well...? (0)

Anonymous Coward | about 5 years ago | (#29025917)

shut up, Ive been waiting for my DNA necklace for years!

Crane (0, Offtopic)

pjt33 (739471) | about 5 years ago | (#28991235)

Time to head down to my local zoo and see whether I can obtain a DNA sample from a specimen of Grus grus.

Hmm...let me see... (0)

Anonymous Coward | about 5 years ago | (#28991287)

...where's that recipe for gray goo. I know it's around here someplace...

Call me dense... (2, Interesting)

Anachragnome (1008495) | about 5 years ago | (#28991325)

I'm missing the application.

Is the idea to create new structures WITHIN the human body(or whatever species, plant, animal, fungus...), or externally, such as another means to create nano-scale devices, but with bio-materials as opposed to non-biological components such as carbon molecules? Both?

It does make sense, either way, as DNA can be coded to self-replicate making any manufacturing processes far easier.

And yes, I am aware that biological entities are, for the most part, made of carbon molecules, at least here on Earth.

Re:Call me dense... (1)

spun (1352) | about 5 years ago | (#28991493)

They are just using DNA as a structural element. You can evidently fold it into all sorts of interesting shapes. Consider this a kind of nano-scale erector set. Motors, computers, power supplies, and other interesting parts sold separately.

Re:Call me dense... (1)

Anachragnome (1008495) | about 5 years ago | (#28991521)

I understand that, but what I don't understand is the advantage this method has over current technology, i.e. carbon deposition techniques, etc. other then the replication factor.

Is the replication factor the sole advantage?

Re:Call me dense... (2, Informative)

Anonymous Coward | about 5 years ago | (#28991703)

I'm not sure about other techniques, but these DNA nanostructures can create potentially any 3-D (and to me, deposition sounds like a 2-D process, with a very tediuous 3-D aspect). I'm fairly certain that the combination of ease of use, manufacturing, and customizability is unmatched by any other technology, but feel free to correct me.

The talk I attended by William Shih had excellent AFM pictures of various 3-d shapes, including a trojan horse(think wooden sculpture). However, he did mention that the more complicated the structure, the longer it took to "cure", or go from mixture of oligos and structural strands to the completed form.

One particular application I could see this making significant headway into would be gene therapy. Cationic liposomes are currently the most effective vectors, but they are very toxic, among other negative qualities. DNA capsules may be more effective, especially if capsules can be easily modified for different payloads.

Re:Call me dense... (1)

Anachragnome (1008495) | about 5 years ago | (#28991941)

So, the tech is a solution to MULTIPLE problems, across multiple disciplines. Now I get it.

"(and to me, deposition sounds like a 2-D process, with a very tediuous 3-D aspect)"

Yeah, that was my take on it as well, and my assumed application for the tech in question. A replacement for tech that wasn't very efficient. I just wasn't sure.

Re:Call me dense... (1)

Onymous Coward (97719) | about 5 years ago | (#28993635)

This fellow, Paul Rothemund, may have developed this technique before Technische Universitaet Muenchen: http://www.dna.caltech.edu/~pwkr/ [caltech.edu]

Here's a TED speech on it. Gives a more detailed idea of how it's meant to be used for construction: http://www.youtube.com/watch?v=Yn1snjEtk54 [youtube.com]

Surprised this hasn't been mentioned. Especially since they're trying to credit T.U.M. with the technique.

Re:Call me dense... (1)

Anachragnome (1008495) | about 5 years ago | (#28993725)

Yeah, what gives?

I hope this guy (and the other people he credits on his page) make a stink about that. Most certainly a lot of funding involved in this, and falsely claiming credit is akin to stealing dude's Pop-Tarts right out of his toaster.

Is it possible such research can be happening along two parallel courses with no awareness of each other? I somehow find that hard to believe.

Re:Call me dense... (0)

Anonymous Coward | about 5 years ago | (#28994587)

Paul Rothemund developed the basic technique for creating 2D objects folded from DNA. This team extended this to 3D nanoconstruction.

Excellent. (1)

FlyingSquidStudios (1031284) | about 5 years ago | (#28991341)

Now all that is needed is to figure out a way to replicate those shapes into an army of giant monsters to do my evil bidding!

Prone to UV light? (3, Interesting)

modrzej (1450687) | about 5 years ago | (#28991455)

I wonder what is a half-life of such a macromolecule. Not an expert in the field, but during my first biochemistry course I was taught that DNA is only kinetically stable (in contrast with thermodynamic stability), so there is a chance that when making its shape extremely fancy, it becomes useless ephemeral compound. There are also mutations caused by interaction with high-energetic photons (UV light) which constantly appear and are repaired in human cells, but may cause obstacles when there's no natural maintenance system as in cells. This may not be the case because mutations may occur extremely rarely in the timescale of nanomachines activity, but thats what I'm curious about.

Re:Prone to UV light? (2)

Vesvvi (1501135) | about 5 years ago | (#28993077)

Most highly-ordered large biomolecules are not "thermodynamically stable", since it takes so much entropy to maintain them (which is to say that the entropy is low). Some exceptions might be nasty molecules like prions or amyloids, which tend to form extended fibers and sheets, with very negative effects.

But kinetic stability can lead to effective thermodynamic stability due to some unique effects. For example, there can be a kinetic barrier to disassembly of a large biomolecule because it's tough to remove that first subunit. Once the first subunit is gone, the "chink in the armor" allows the whole thing to begin to fall apart. But because the whole assembly is stable until the first one leaves, it has the effect of being globally stable.

But getting back to the big picture, DNA can be very stable, as evidenced by recovery of DNA more than thousands of years old. Of course it won't be retaining complex quaternary structures like those developed by the researchers. On the other hand, it's very desirable to have nanostructures with a finite lifetime, especially one that can be controlled. If it's used for drug delivery packaging, you might want it to last only a few days. If it's a template for hard materials (iron-based magnetic structures, for example), you might want to be able to cause it to fall apart intentionally within a few hours. DNA isn't really a good candidate for permanent nanomaterials, since it can be degraded both passively and actively by quite a few different pathways.

Folding@Home? (2, Interesting)

johnthorensen (539527) | about 5 years ago | (#28991609)

I'm just curious, did the researchers draw upon any of the Folding@Home work for this? Seems like simulating these sorts of interactions is sort of the point. I know F@H is primarily looking at proteins but just curious if any of the knowledge crosses over. Of course, 'Folding@Home' would make a great name for the desktop rapid prototyping machine based on this work. :)

Re:Folding@Home? (0)

Anonymous Coward | about 5 years ago | (#28991813)

This is not the same field as Folding @ Home, which is protein structure prediction. Protein structure prediction is hard because not only do we not completely understand protein structure stability, but there are also an enormous amount of possible protein structures for a given protein.

This is simply taking DNA, creating sheets by having a structural DNA weave back and forth with oligonucleotides specifically designed to "staple" the edges, no mystery about it.

Re:Folding@Home? (1)

StellarFury (1058280) | about 5 years ago | (#28993017)

Yeah, except proteins aren't made out of nucleic acids, don't have a double helix structure, follow virtually none of the same rules as polypeptides... you get the picture.

DNA is in an entirely different section of the Central Dogma from proteins. Folding@Home doesn't really apply, especially because Folding@Home is designed primarily for determining quaternary structure (the real "folding" part of proteins), which these things can't even develop.

Also, Folding@Home is not the first of its kind. It's part of a long tradition of molecular visualization that started shortly after the computer was invented, though the ideas were born with quantum mechanics. Blame Schroedinger, really.

You can probably model these systems ab initio, given a single computer with a buff enough processor and a nice GPU or two - and maybe a few hours of computer time. You don't need supercomputing or distributed processing.

Link to caDNAno software (2, Informative)

structural_biologist (1122693) | about 5 years ago | (#28991627)

The research team that produced the paper in Science paper (link [doi.org] (subscription required to see more than the abstract)) described in the science daily writeup also published a paper in Nature (link [doi.org] ) that more fully describes their method of creating three dimensional objects out of DNA (the newest paper expands these methods to construct more complicated objects with more precise curvature). Furthermore, they have published the open-source software that they used to design the DNA nanostructures (http://cadnano.org/). I was at a talk by the lead author of the Nature paper who said that, using their software, a high school student was able to design one of the structures they used in the paper as a summer project.

Too many ... on the dance floor (1)

barocco (1168573) | about 5 years ago | (#28991655)

The only boob I'd see tonight will not only be made of origami, but also nano-scale.

Grey Goo... (0)

garun (1479865) | about 5 years ago | (#28991669)

this experiments at one time could be very dangerous - look in wiki for Grey Goo
it could just mutate - to be uncontrollable - and it is simple recipe to extinct all humanity - I hope that will not happen during my life..

Re:Grey Goo... (1)

StellarFury (1058280) | about 5 years ago | (#28993031)

Pure FUD. Someone mod this down.

Nearly identical to a previous topic (1)

Vesvvi (1501135) | about 5 years ago | (#28992131)

Here's the older topic:http://science.slashdot.org/article.pl?sid=09/05/08/0344248

And the older scientific publication: http://www.nature.com/nature/journal/v459/n7243/full/nature07971.html [nature.com]

The real difference in this publication compared to the previous one is that these researchers are making really compact bundles [sciencedaily.com] while the previous ones have more flexible (probably) hollow structures dependent on key localized interactions. These are more likely driven by the summation of lots of little effects.

Without having read the article yet, it seems to be a common theme of top-down vs bottom-up design, which is a topic that crops up frequently.

O.o (1)

stonedcat (80201) | about 5 years ago | (#28992357)

Nanogami? I like the sound of that!

Sounds bad (1)

lawpoop (604919) | about 5 years ago | (#28993555)

Call me a luddite, but this sounds bad, in a hybrid nanotech-grey-goo GM Crop mash-up kind of way.

If they're using these DNA orgami structures in cells, what are the chances that there will be harmful combinations of DNA peeling of and doing all kinds of whatever inside your cells?

If they are using these outside of organisms, what are the chances that random bacteria are just going to slurp up these bits of DNA and do all kinds of whatever with them? Actually, that sounds less bad than using them in humans.

CAD/CAM (1)

onwardknave (533210) | about 5 years ago | (#28995133)

"With the right software, organism design should be indistinguishable from CAD/CAM." -Dr. Donovan (from Deus Ex, in the MJ12 Labs)

Could it be? (1)

lightinthedark (1557699) | about 5 years ago | (#29008515)

"They had mastered the ultimate technology, the ability to alter physical reality by will alone. They called this ability "tuning". But they were dying. Their civilization was in decline..."
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